From 56ef0d40fcbce76b5a2cb95ba9a5f0e49856bb04 Mon Sep 17 00:00:00 2001
From: athomps <athomps@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 22 Jan 2016 03:14:16 +0000
Subject: [PATCH] Added description of peratom keyword
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14469 f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/compute_voronoi_atom.txt | 29 ++++++++++++++++++++---------
1 file changed, 20 insertions(+), 9 deletions(-)
diff --git a/doc/compute_voronoi_atom.txt b/doc/compute_voronoi_atom.txt
index b97106aa0a..dadabeb47c 100644
--- a/doc/compute_voronoi_atom.txt
+++ b/doc/compute_voronoi_atom.txt
@@ -15,7 +15,8 @@ compute ID group-ID voronoi/atom keyword arg ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
voronoi/atom = style name of this compute command :l
zero or more keyword/value pairs may be appended :l
-keyword = {only_group} or {surface} or {radius} or {edge_histo} or {edge_threshold} or {face_threshold} :l
+keyword = {only_group} or {surface} or {radius} or {edge_histo} or {edge_threshold}
+or {face_threshold} or {neighbors} or {peratom} :l
{only_group} = no arg
{occupation} = no arg
{surface} arg = sgroup-ID
@@ -29,7 +30,8 @@ keyword = {only_group} or {surface} or {radius} or {edge_histo} or {edge_thresho
minlength = minimum length for an edge to be counted
{face_threshold} arg = minarea
minarea = minimum area for a face to be counted
- {neighbors} value = {yes} or {no} = store list of all neighbors or no :pre
+ {neighbors} value = {yes} or {no} = store list of all neighbors or no
+ {peratom} value = {yes} or {no} = per-atom quantities accessible or no :pre
:ule
[Examples:]
@@ -46,14 +48,16 @@ compute 6 all voronoi/atom neighbors yes
Define a computation that calculates the Voronoi tessellation of the
atoms in the simulation box. The tessellation is calculated using all
atoms in the simulation, but non-zero values are only stored for atoms
-in the group.
+in the group.
-By default two quantities per atom are calculated by this compute.
+By default two per-atom quantities are calculated by this compute.
The first is the volume of the Voronoi cell around each atom. Any
point in an atom's Voronoi cell is closer to that atom than any other.
The second is the number of faces of the Voronoi cell. This is
equal to the number of nearest neighbors of the central atom,
-plus any exterior faces (see note below).
+plus any exterior faces (see note below). If the {peratom} keyword
+is set to "no", the per-atom quantities are still calculated,
+but they are not accessible.
:line
@@ -180,15 +184,16 @@ when using the "create_box"_create_box.html or
[Output info:]
-This compute calculates a per-atom array with 2 columns. In regular
+By default, this compute calculates a per-atom array with 2 columns. In regular
dynamic tessellation mode the first column is the Voronoi volume, the
second is the neighbor count, as described above (read above for the
output data in case the {occupation} keyword is specified).
These values can be accessed by any command that
uses per-atom values from a compute as input. See "Section_howto
15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
-
+options. If the {peratom} keyword is set to "no", the
+per-atom array is still created, but it is not accessible.
+
If the {edge_histo} keyword is used, then this compute
generates a global vector of length {maxedge}+1, containing
a histogram of the number of edges per face.
@@ -197,6 +202,12 @@ If the {neighbors} value is set to yes, then
this compute calculates a local array with 3 columns. There
is one row for each face of each Voronoi cell.
+In LAMMPS contexts such as "compute reduce"_compute_reduce.html that can
+accept either a per-atom vector quantity or a local vector
+quantity, the behavior depends on the value gives for the {peratom}
+keyword: for the default value "yes" the per-atom array is accessed,
+for the value {no} the local array is accessed.
+
The Voronoi cell volume will be in distance "units"_units.html cubed.
The Voronoi face area will be in distance "units"_units.html squared.
@@ -210,4 +221,4 @@ LAMMPS"_Section_start.html#start_3 section for more info.
"dump custom"_dump.html, "dump local"_dump.html
-[Default:] none
+[Default:] {neighbors} no, {peratom} yes
--
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